AMBER Archive (2006)

Subject: AMBER: RMSd error

From: Claire Zerafa (cporteli_at_waldonet.net.mt)
Date: Mon May 22 2006 - 03:52:34 CDT

Hi amber users,

I am analysing a trajectory spanning 1860ps divided into 11 stages. My input ptraj script to calculate RMSd is as shown below, (THERE WAS NO LINE BREAK AT THE @CA POINT) and it worked fine when I worked with a first equilibrium 20ps run. When I run this script, I only get RMSd values for 479.6 out of the 1860ps trajectory, and when I tried to run a similar script with a similar trajectory with the same time span the RMSd values got dumped over 720ps. Can anyone tell me why this happens please? The only error message I get is the following:

ERROR in dispatchToken: Token string "undocked_calc_backbone_rms.in" not
found in tokenlist
but then all seems to proceed as normal....

PTRAJ: Successfully read in 2398 sets and processed 2398 sets.
       Dumping accumulated results (if any)

PTRAJ RMS: dumping RMSd vs time data

Thanks

Claire

undocked_calc_backbone_rms.in
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md2.mdcrd.gz
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md3.mdcrd.gz
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md4.mdcrd.gz
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md5.mdcrd.gz
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md6.mdcrd.gz
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md7.mdcrd.gz
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md8.mdcrd.gz
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md9.mdcrd.gz
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md10.mdcrd.gz
rms first out
/DATA/VINCLOZOLIN_TRAJECTORY_ANALYSIS/vinclozolin_backbone.rms @CA time 0.2
strip :WAT
go

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